F.est.efficiency: F.est.efficiency

In tmcd82070/CAMP_RST: CAMP RST R Routines

F.est.efficiency

Description

Estimate trap efficiency for every sample period, per trap.

Usage

F.est.efficiency(
  release.df,
  batchDate,
  df.spline = 4,
  plot = TRUE,
  plot.file = NA
)

Arguments

release.df	A data frame produced by F.get.release.data. Contains information on releases and recaptures. This data frame has one line per release trial per trap, with trap identified via variable TrapPositionID.
batchDate	A POSIX-formatted vector of dates.
df.spline	The default degrees of freedom to use in the estimation of splines. Default is 4 (1 internal knot).
plot	A logical indicating if efficiencies are to be plotted over time, per trap.
plot.file	The name to which a graph of efficiency is to be output, if plot=TRUE.

Details

Generally, fish released as part of an efficiency trial arrive in traps over the course of several days. F.est.efficiency calculates the mean recapture time of all re-captured fish. When a release trial resulted in no recaptures, the mean recapture time is half way between the first and last visit of the trial (i.e., after release).

Function F.assign.batch.date assigns mean recapture time, which is mesured to the nearest minute, to a batchDate. Batch date a simple calendar date.

Fishing instances during which traps utilized half-cones are recorded in variable HalfCone. During these instances, the number of captured fish, variable Recaps, is multiplied by the value of halfConeMulti. The value of halfConeMulti is set in GlobalVars and defaults to 2. The expansion by halfConeMulti happens on the raw catch, and not the mean recapture. In this way, the number recorded in variable Recaps may not be twice the number recorded in variable oldRecaps.

Note that the run season sample period is a vector of length 2 of dates, housing the beginning and ending of the run. These are stored as an attribute of the release.df data frame.

Value

A data frame containing fishing intervals and associated capture efficiency, along with variable gam.estimated. Variable gam.estimated is "Yes" if efficiency for that interval was estimated by the GAM model (method=3), rather than being empirical (method=1).

Author(s)

WEST Inc.

See Also

F.get.release.data, F.assign.batch.date

Examples

## Not run: 
#   ---- Estimate the efficiency.  
theEff <- F.est.efficiency(release.df,batchDate,df.spline=4,plot=TRUE,plots.file=NA)

## End(Not run)

tmcd82070/CAMP_RST documentation built on April 6, 2022, 12:07 a.m.